EzCatDB: M00173
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DB codeM00173
RLCP classification3.103.90020.1135 : Transfer
CATH domainDomain 13.30.420.10 : Nucleotidyltransferase; domain 5
Domain 21.20.1060.10 : Taq DNA Polymerase; Chain T, domain 4
Domain 33.30.70.370 : Alpha-Beta PlaitsCatalytic domain
Domain 41.10.150.20 : DNA polymerase; domain 1Catalytic domain
E.C.2.7.7.7

CATH domainRelated DB codes (homologues)
1.10.150.20 : DNA polymerase; domain 1M00055,M00104,M00175,M00208,D00158
1.20.1060.10 : Taq DNA Polymerase; Chain T, domain 4M00055,M00175
3.30.420.10 : Nucleotidyltransferase; domain 5M00206,T00252,M00019,M00020,M00055,M00135,M00146,M00166,M00175,M00186
3.30.70.370 : Alpha-Beta PlaitsM00055,M00104,M00175

Enzyme Name
UniProtKBKEGG

P00581
Protein nameDNA polymeraseDNA-directed DNA polymerase
DNA polymerase I
DNA polymerase II
DNA polymerase III
DNA polymerase alpha
DNA polymerase beta
DNA polymerase gamma
DNA nucleotidyltransferase (DNA-directed)
DNA nucleotidyltransferase (DNA-directed)
deoxyribonucleate nucleotidyltransferase
deoxynucleate polymerase
deoxyribonucleic acid duplicase
deoxyribonucleic acid polymerase
deoxyribonucleic duplicase
deoxyribonucleic polymerase
deoxyribonucleic polymerase I
DNA duplicase
DNA nucleotidyltransferase
DNA polymerase
DNA replicase
DNA-dependent DNA polymerase
duplicase
Klenow fragment
sequenase
Taq DNA polymerase
Taq Pol I
Tca DNA polymerase
SynonymsEC 2.7.7.7
T7 DNA polymerase
RefSeqNP_041982.1 (Protein)
NC_001604.1 (DNA/RNA sequence)
PfamPF00476 (DNA_pol_A)
[Graphical view]

KEGG pathways
MAP codePathways
MAP00230Purine metabolism
MAP00240Pyrimidine metabolism

UniProtKB:Accession NumberP00581
Entry nameDPOL_BPT7
ActivityDeoxynucleoside triphosphate + DNA(n) = diphosphate + DNA(n+1).
SubunitComposed of two subunits. One is encoded by the phage and the other is encoded by the host thioredoxin.
Subcellular location
Cofactor

Compound table: links to PDB-related databases & PoSSuM

CofactorsSubstratesProducts
KEGG-idC00305C00677C00039C00013C00039
CompoundMagnesiumDeoxynucleoside triphosphateDNA(n)PyrophosphateDNA(n+1)
Typedivalent metal (Ca2+, Mg2+)nucleotidenucleic acidsphosphate group/phosphate ionnucleic acids
ChEBI18420


29888

PubChem888


21961011
1023

             
1t7pA01UnboundUnboundUnboundUnboundUnbound
1skrA01UnboundUnboundUnboundUnboundUnbound
1sksA01UnboundUnboundUnboundUnboundUnbound
1skwA01UnboundUnboundUnboundUnboundUnbound
1sl0A01UnboundUnboundUnboundUnboundUnbound
1sl0C01UnboundUnboundUnboundUnboundUnbound
1sl1A01UnboundUnboundUnboundUnboundUnbound
1sl2A01UnboundUnboundUnboundUnboundUnbound
1t8eA01UnboundUnboundUnboundUnboundUnbound
1tk0A01UnboundUnboundUnboundUnboundUnbound
1tk5A01UnboundUnboundUnboundUnboundUnbound
1tk8A01UnboundUnboundUnboundUnboundUnbound
1tkdA01UnboundUnboundUnboundUnboundUnbound
1x9mA01UnboundUnboundUnboundUnboundUnbound
1x9sA01UnboundUnboundUnboundUnboundUnbound
1x9wA01UnboundUnboundUnboundUnboundUnbound
1t7pA02UnboundUnboundUnboundUnboundUnbound
1skrA02UnboundUnboundUnboundUnboundUnbound
1sksA02UnboundUnboundUnboundUnboundUnbound
1skwA02UnboundUnboundUnboundUnboundUnbound
1sl0A02UnboundUnboundUnboundUnboundUnbound
1sl0C02UnboundUnboundUnboundUnboundUnbound
1sl1A02UnboundUnboundUnboundUnboundUnbound
1sl2A02UnboundUnboundUnboundUnboundUnbound
1t8eA02UnboundUnboundUnboundUnboundUnbound
1tk0A02UnboundUnboundUnboundUnboundUnbound
1tk5A02UnboundUnboundUnboundUnboundUnbound
1tk8A02UnboundUnboundUnboundUnboundUnbound
1tkdA02UnboundUnboundUnboundUnboundUnbound
1x9mA02UnboundUnboundUnboundUnboundUnbound
1x9sA02UnboundUnboundUnboundUnboundUnbound
1x9wA02UnboundUnboundUnboundUnboundUnbound
1t7pA03Bound:2x_MGUnboundAnalogue:G-C-C-A-G-T-G-C-C-A-2DA(chain P)UnboundUnbound
1skrA03Bound:2x_MGUnboundAnalogue:G-C-C-A-G-T-G-C-C-A-2DA(chain P)UnboundUnbound
1sksA03UnboundUnboundAnalogue:G-G-C-C-A-G-T-G-C-C-2DT(chain P)UnboundUnbound
1skwA03UnboundUnboundAnalogue:C-A-G-T-G-C-C-2DT(chain P)UnboundUnbound
1sl0A03UnboundUnboundAnalogue:G-G-C-C-A-G-T-G-C-C-2DT(chain P)UnboundUnbound
1sl0C03UnboundUnboundAnalogue:G-G-C-C-A-G-T-G-C-C-2DT(chain Q)UnboundUnbound
1sl1A03UnboundUnboundAnalogue:C-A-G-T-G-C-C-T-2DA(chain P)UnboundUnbound
1sl2A03Bound:2x_MGUnboundAnalogue:C-A-G-T-G-C-C-T-2DA(chain P)UnboundUnbound
1t8eA03Bound:2x_MGUnboundAnalogue:C-G-A-A-A-A-C-G-A-C-G-G-C-C-A-G-T-G-C-C-A-2DT(chain C)UnboundUnbound
1tk0A03Bound:2x_MGUnboundAnalogue:C-G-G-C-C-A-G-T-G-C-C-A-DDG(chain P)UnboundUnbound
1tk5A03UnboundUnboundAnalogue:G-C-C-A-G-T-G-C-C-A-DDG(chain P)UnboundUnbound
1tk8A03Bound:2x_MGUnboundAnalogue:A-C-G-A-C-G-G-C-C-A-G-T-G-C-C-A-2DA(chain P)UnboundUnbound
1tkdA03Bound:2x_MGUnboundAnalogue:C-G-A-C-G-G-C-C-A-G-T-G-C-C-A-DOC(chain C)UnboundUnbound
1x9mA03UnboundUnboundAnalogue:G-T-A-G-T-G-T-G-A-2DT(chain C)UnboundUnbound
1x9sA03UnboundUnboundAnalogue:G-G-T-A-G-T-G-T-G-A-2DT(chain P)UnboundUnbound
1x9wA03UnboundUnboundAnalogue:G-G-T-A-G-T-G-T-G-A-2DT(chain C)UnboundUnbound
1t7pA04UnboundAnalogue:DG3UnboundUnboundUnbound
1skrA04UnboundAnalogue:DADUnboundUnboundUnbound
1sksA04UnboundUnboundUnboundUnboundUnbound
1skwA04UnboundUnboundUnboundUnboundUnbound
1sl0A04UnboundAnalogue:DADUnboundUnboundUnbound
1sl0C04UnboundAnalogue:DADUnboundUnboundUnbound
1sl1A04UnboundUnboundUnboundUnboundUnbound
1sl2A04UnboundAnalogue:DADUnboundUnboundUnbound
1t8eA04UnboundAnalogue:DCTUnboundUnboundUnbound
1tk0A04UnboundAnalogue:DCTUnboundUnboundUnbound
1tk5A04UnboundUnboundUnboundUnboundUnbound
1tk8A04UnboundAnalogue:D3TUnboundUnboundUnbound
1tkdA04UnboundAnalogue:D3TUnboundUnboundUnbound
1x9mA04UnboundUnboundUnboundUnboundUnbound
1x9sA04UnboundUnboundUnboundUnboundUnbound
1x9wA04UnboundUnboundUnboundUnboundUnbound

Active-site residues
resource
PDB;1kfn, 1krp, 1ksp, 2kfn, 2kfz, 2kzm, 2kzz & literature [25]
pdbCatalytic residuesCofactor-binding residuesMain-chain involved in catalysis
           
1t7pA01 
 
 
1skrA01 
 
 
1sksA01 
 
 
1skwA01 
 
 
1sl0A01 
 
 
1sl0C01 
 
 
1sl1A01 
 
 
1sl2A01 
 
 
1t8eA01 
 
 
1tk0A01 
 
 
1tk5A01 
 
 
1tk8A01 
 
 
1tkdA01 
 
 
1x9mA01 
 
 
1x9sA01 
 
 
1x9wA01 
 
 
1t7pA02 
 
 
1skrA02 
 
 
1sksA02 
 
 
1skwA02 
 
 
1sl0A02 
 
 
1sl0C02 
 
 
1sl1A02 
 
 
1sl2A02 
 
 
1t8eA02 
 
 
1tk0A02 
 
 
1tk5A02 
 
 
1tk8A02 
 
 
1tkdA02 
 
 
1x9mA02 
 
 
1x9sA02 
 
 
1x9wA02 
 
 
1t7pA03 
ASP 475;ALA 476;ASP 654(Two Mg2+ binding)
 
1skrA03 
ASP 475;ALA 476;ASP 654(Two Mg2+ binding)
 
1sksA03 
ASP 475;ALA 476;ASP 654(Two Mg2+ binding)
 
1skwA03 
ASP 475;ALA 476;ASP 654(Two Mg2+ binding)
 
1sl0A03 
ASP 475;ALA 476;ASP 654(Two Mg2+ binding)
 
1sl0C03 
ASP 475;ALA 476;ASP 654(Two Mg2+ binding)
 
1sl1A03 
ASP 475;ALA 476;ASP 654(Two Mg2+ binding)
 
1sl2A03 
ASP 475;ALA 476;ASP 654(Two Mg2+ binding)
 
1t8eA03 
ASP 475;ALA 476;ASP 654(Two Mg2+ binding)
 
1tk0A03 
ASP 475;ALA 476;ASP 654(Two Mg2+ binding)
 
1tk5A03 
ASP 475;ALA 476;ASP 654(Two Mg2+ binding)
 
1tk8A03 
ASP 475;ALA 476;ASP 654(Two Mg2+ binding)
 
1tkdA03 
ASP 475;ALA 476;ASP 654(Two Mg2+ binding)
 
1x9mA03 
ASP 475;ALA 476;ASP 654(Two Mg2+ binding)
 
1x9sA03 
ASP 475;ALA 476;ASP 654(Two Mg2+ binding)
 
1x9wA03 
ASP 475;ALA 476;ASP 654(Two Mg2+ binding)
 
1t7pA04HIS 506;ARG 518;LYS 522;TYR 526
 
GLY 478
1skrA04HIS 506;ARG 518;LYS 522;TYR 526
 
GLY 478
1sksA04HIS 506;ARG 518;LYS 522;TYR 526
 
GLY 478
1skwA04HIS 506;ARG 518;LYS 522;TYR 526
 
GLY 478
1sl0A04HIS 506;ARG 518;LYS 522;TYR 526
 
GLY 478
1sl0C04HIS 506;ARG 518;LYS 522;TYR 526
 
GLY 478
1sl1A04HIS 506;ARG 518;LYS 522;TYR 526
 
GLY 478
1sl2A04HIS 506;ARG 518;LYS 522;TYR 526
 
GLY 478
1t8eA04HIS 506;ARG 518;LYS 522;TYR 526
 
GLY 478
1tk0A04HIS 506;ARG 518;LYS 522;TYR 526
 
GLY 478
1tk5A04HIS 506;ARG 518;LYS 522;TYR 526
 
GLY 478
1tk8A04HIS 506;ARG 518;LYS 522;TYR 526
 
GLY 478
1tkdA04HIS 506;ARG 518;LYS 522;TYR 526
 
GLY 478
1x9mA04HIS 506;ARG 518;LYS 522;TYR 526
 
GLY 478
1x9sA04HIS 506;ARG 518;LYS 522;TYR 526
 
GLY 478
1x9wA04HIS 506;ARG 518;LYS 522;TYR 526
 
GLY 478

References for Catalytic Mechanism
ReferencesSectionsNo. of steps in catalysis
[1]p.254-256
[2]Fig.4, p.61

references
[1]
CommentsX-RAY CRYSTALLOGRAPHY (2.2 ANGSTROMS)
Medline ID98101638
PubMed ID9440688
JournalNature
Year1998
Volume391
Pages251-8
AuthorsDoublie S, Tabor S, Long AM, Richardson CC, Ellenberger T
TitleCrystal structure of a bacteriophage T7 DNA replication complex at 2.2 A resolution.
Related PDB1t7p
Related UniProtKBP00581
[2]
PubMed ID9519297
JournalCurr Opin Struct Biol
Year1998
Volume8
Pages54-63
AuthorsBrautigam CA, Steitz TA
TitleStructural and functional insights provided by crystal structures of DNA polymerases and their substrate complexes.
[3]
PubMed ID15235589
JournalNat Struct Mol Biol
Year2004
Volume11
Pages784-90
AuthorsLi Y, Dutta S, Doublie S, Bdour HM, Taylor JS, Ellenberger T
TitleNucleotide insertion opposite a cis-syn thymine dimer by a replicative DNA polymerase from bacteriophage T7.
Related PDB1skr,1sks,1skw,1sl0,1sl1,1sl2
[4]
PubMed ID15297882
JournalEMBO J
Year2004
Volume23
Pages3452-61
AuthorsBrieba LG, Eichman BF, Kokoska RJ, Doublie S, Kunkel TA, Ellenberger T
TitleStructural basis for the dual coding potential of 8-oxoguanosine by a high-fidelity DNA polymerase.
Related PDB1t8e,1tk0,1tk5,1tk8,1tkd
[5]
PubMed ID15528277
JournalProc Natl Acad Sci U S A
Year2004
Volume101
Pages16186-91
AuthorsDutta S, Li Y, Johnson D, Dzantiev L, Richardson CC, Romano LJ, Ellenberger T
TitleCrystal structures of 2-acetylaminofluorene and 2-aminofluorene in complex with T7 DNA polymerase reveal mechanisms of mutagenesis.
Related PDB1x9m,1x9s,1x9w

comments
This enzyme belongs to the DNA polymerase type-A family.
Although this enzyme belongs to the DNA polymerase type-A family, giving different global structure from that of the type-B family, the active site is very similar to that of type-B family. Thus, the catalytic mechanism must be similar to that of type-B family (M00019, M00020 in EzCatDB).
According to the literature [1] & [2], the catalytic reaction of polymerase domains proceeds as follows:
(1) The metal ion A (bound to Asp475 & Asp654) activates 3'-OH of DNA by lowering its pKa.
(2) The activated 3'-O atom makes a nucleophilic attack on the alpha-phosphate group of dNTP, forming a pentacoordinated transition-state.
(3) The negative charges on the transferred group (alpha-phoshate) and the leaving group (beta-phosphate and gamma-phosphate) are stabilized by the metal ions and stabilizers on the fourth domain (Gly478, His506, Arg518, Lys522, & Tyr526). According to the literature [1], Lys522 stabilizes the transferred alpha-phosphate, which is also stabilzed by both A and B metal ions. His506 and Tyr526 stabilize beta-phosphate, along with the metal ion B, Arg518 stabilizes gamma-phosphate together with the metal ion B (see [1]).

createdupdated
2004-03-032009-02-26


Copyright: Nozomi Nagano, JST & CBRC-AIST
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Funded by Grant-in-Aid for Publication of Scientific Research Results/Japan Society for the Promotion of Science (JSPS) (April 2005 - March 2006)
Funded by Grant-in-Aid for Scientific Research (B)/Japan Society for the Promotion of Science (JSPS) (April 2005 - March 2008)
Funded by BIRD/Japan Science and Technology Corporation (JST) (September 2005 - September 2008)
Funded by BIRD/Japan Science and Technology Corporation (JST) (October 2007 - September 2010)
Funded by Grant-in-Aid for Publication of Scientific Research Results/Japan Society for the Promotion of Science (JSPS) (April 2011 - March 2012)
Funded by Grant-in-Aid for Publication of Scientific Research Results/Japan Society for the Promotion of Science (JSPS) (April 2012 - March 2013)
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